rs1971773

Variant names:

• chr17-8729992-C-T
• rs1971773
• NM_144681.3:c.*138G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144681.3(CCDC42):​c.*138G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 717,498 control chromosomes in the GnomAD database, including 48,714 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (8660 hom., cov: 33)
  • Exomes 𝑓: 0.37 (40054 hom.)
• Consequence: CCDC42 NM_144681.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

CCDC42 (HGNC:26528): (coiled-coil domain containing 42) Predicted to be involved in spermatid development. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC42	NM_144681.3	c.*138G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000293845.8	NP_653282.2
CCDC42	NM_001158261.2	c.*138G>A		3_prime_UTR_variant	Exon 6 of 6		NP_001151733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC42	ENST00000293845	c.*138G>A		3_prime_UTR_variant	Exon 7 of 7	2	NM_144681.3	ENSP00000293845.3
CCDC42	ENST00000539522	c.*138G>A		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000444359.2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49021 AN: 152052 Hom.: 8656 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.366 AC: 206928 AN: 565328 Hom.: 40054 Cov.: 7 AF XY: 0.365 AC XY: 111138 AN XY: 304182

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.610

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.439

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.407

Gnomad4 NFE exome AF: 0.331

Gnomad4 OTH exome AF: 0.349

GnomAD4 genome AF: 0.322 AC: 49042 AN: 152170 Hom.: 8660 Cov.: 33 AF XY: 0.331 AC XY: 24629 AN XY: 74378

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.322

Alfa AF: 0.343 Hom.: 12622

Bravo AF: 0.326

Asia WGS AF: 0.397 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1971773; hg19: chr17-8633310;